The two sometimes-separate consciousnesses were an artifact of the awakening of the Countermeasure; it used existing processes/agents as part of how it hid from the Blight.
We are wildlife that must not be noticed by the overness, by the Power that soon will be. On some nodes they shrank to smallness and almost remembered humanity, became echoes....
Once upon a time we were copies of those two. Once upon a time just weeks ago when the archaeologists started the ego-level programs.
So they started out as personal avatars/agents of Sjana and Arne. They were enabled to survive and hide from the Blight by the Countermeasure itself. They even discuss this:
"Still," thought the hopeful one, the one who always looked for the craziest outs, "we should not be. The evil should long ago have found us."
"The evil is young, barely three days old."
"Still. We exist. It proves something. The humans found more than a great evil in this archive."
"Perhaps they found two.
"Or an antidote." Whatever else, the overness was missing some things and misinterpreting others.
The Blight itself reflects on how it missed things:
Long seconds probing the archives. There were gaps, checksums damaged. Some of the damage was age....
But some of the damage was created by the Countermeasure to hide its departure on the human ship.
Yes, there were blindspots, carefully installed from the beginning, and not by the humans. Two had been born here. Itself... and the poison, the reason for its fall of old.
Note that Pham speaks of the ghosts in the past tense; they existed when the Countermeasure fled from the High Lab, but aren't there anymore. He's simply relaying something from a memory of them:
"A thousand light-years? Ten thousand? I'm not sure. The ghosts in Countermeasure - Arne and Sjana thought it might rise so high it would punch into the Transcend, encyst the Blight right where it sits.... That must be what happened Before."